In this article, the author clearly uses the hacker to mount an ad hominem attack on the entire technology industry, programmers etc. giving examples of Fortune 500 companies being damaged by individuals who illegitimately took down the sites of those companies. The author was basically saying "See, Mark Zuckerberg, the CEO of Facebook is a hacker. This is why Silicon Valley is wrong in supporting SOPA, since they are on the same side as people who damaged Fortune 500 companies."
In the general sense, I think it comes from the public's condescending view on people who are legitimate and call themselves hackers, like on hacker news. For example, if I'm on Hacker News on my phone on the way to school, and one of peers sees me on there, he gives me a weird look and assumes it's the illegitimate form of "hacker". Even my dad was worried when he saw me on Hacker News, saying "Stay away from there." Obviously he thought it was community for the illegitimate form of hacking. Even after I explained the real meaning to him, he was still quite suspicious.
In the general sense, I think it comes from the public's condescending view on people who are legitimate and call themselves hackers, like on hacker news. For example, if I'm on Hacker News on my phone on the way to school, and one of peers sees me on there, he gives me a weird look and assumes it's the illegitimate form of "hacker". Even my dad was worried when he saw me on Hacker News, saying "Stay away from there." Obviously he thought it was community for the illegitimate form of hacking. Even after I explained the real meaning to him, he was still quite suspicious.